Missing save file in-game

[Ozymandias]

I decided to play some Majora's Mask in Zelda: Collector's Edition after a hiatus of about a year. The only problem is, when I go into the game to load my save, there are no saves showing up. I haven't changed anything; just booted up Dolphin 5.0 and started up the game. I assumed that all my old saves were lost or just messed up, but I checked the memory card and there are a bunch of saves there, including my save from Majora's Mask. There are also a few saves from Ocarina of Time on the same game that show up and play just fine. So maybe just that one file is corrupted?. . . Is there a way to repair a specific save file or is there something else I might try to find what the problem is and fix it? I did try to copy the file over and play it on another memory card. When I tried that, the game said my memory card was corrupted and had to be reformatted. I'm not sure if that had to do with the actual save file or my brutish method of switching memory cards, though(changing file names). Any ideas? Not life or death, but I'd rather not restart the whole game if at all possible.
Thanks in advance!

[leolam]

Could you show a screenshot of the GameCube tab (in the Configuration window)?

[Ozymandias]

Here is the GC Configuration screen. Is this what you needed? The save file is in both memory cards.

[leolam]

In both memory cards? That sounds like it could break stuff...

What happens if you disable slot B, and choose MemoryCardB.USA.raw for slot A?

[Ozymandias]

I disabled slot B and set card B to slot A, as you said. It still didn't work, unfortunately. Just to be sure, I copied over an Ocarina of Time file, which loaded perfectly. I did notice something really interesting in playing around with it though. When you go to play one of the games, like Majora's Mask or Ocarina of time, after loading the disk it apparently tries to find and load any existing directory on the memory card. If there is one, you get the screen with the different profiles. If it doesn't detect one, a message comes up stating this and asking if you'd like to create a directory on the memory card for that game. The weird thing is, when I don't have my Majora's Mask file on the card, it displays this message. However, when it is on the card, the profile screen comes up normally. So it does recognize that there is a save directory on the card, but for some reason none of the profiles are populated (and when copy or erase is selected the game says there are no available files to do those actions to). So either my save file was just deleted with the directory being left on the memory card, or there is some kind of trouble with the actual reading of the file. Is there a way to check if there is actually data in the save slot on the memory card? According to memory manager the save takes up 21 blocks, first block being 54, but maybe the game just sets aside that many as soon as you create a save directory?